GenDBWiki/DeveloperDocumentation/ToolIntegration - Revision history

Admin: 40 revisions

2011-10-26T06:16:03Z

40 revisions

← Older revision	Revision as of 08:16, 26 October 2011
(No difference)

imported>AlexanderGoesmann at 15:13, 6 January 2006

2006-01-06T15:13:16Z

← Older revision		Revision as of 17:13, 6 January 2006
Line 16:		Line 16:
	= Currently implemented generic tools =		= Currently implemented generic tools =

	== [[TransTerm]] ==		== [[TransTerm]] (contributed by D. Wetter) ==
	The TransTerm tool finds rho-independent transcription terminators in bacterial genomes. It creates observations, terminator regions (''GENDB::Region::Signal::Terminator'') and automatic annotations.		The TransTerm tool finds rho-independent transcription terminators in bacterial genomes. It creates observations, terminator regions (''GENDB::Region::Signal::Terminator'') and automatic annotations.

	=== Requirements ===		=== Requirements ===
	* GlobalConfig.pm (''GENDB/Common'')		* edit GlobalConfig.pm (located in ''GENDB/Common/'' directory)
	* [[Media:GenDBWiki$$DeveloperDocumentation$$ToolIntegration$TransTerm.pm\|TransTerm].pm] (''GENDB/Tools'')
	* [[Media:GenDBWiki$$DeveloperDocumentation$$ToolIntegration$create_generic_tool_TransTerm.pl\|create_generic_tool_TransTerm.pl]] (''GENDB/exec'')		add the following lines to your GenDB configuration:

			<pre><nowiki>

			our @EXPORT_OK=qw(... GENDB_TRANSTERM GENDB_TRANSTERM_LIB ...)

			...

			=item * GENDB_TRANSTERM, GENDB_TRANSTERM_LIB

			pathname to TransTerm script and directory containing binaries and scripts from TransTerm package

			=cut

			use constant GENDB_TRANSTERM => '/PATH/TO/YOUR//INSTALLATION/OF/TransTerm';
			use constant GENDB_TRANSTERM_LIB => '/LIBRARYPATH/TO/YOUR//INSTALLATION/OF/TransTerm';
			</nowiki></pre>


			* [[Media:GenDBWiki$$DeveloperDocumentation$$ToolIntegration$TransTerm.pm.txt\|TransTerm].pm] (copy to ''GENDB/Tools'' directory)
			* [[Media:GenDBWiki$$DeveloperDocumentation$$ToolIntegration$create_generic_tool_TransTerm.pl\|create_generic_tool_TransTerm.pl]] (copy to ''GENDB/exec'' directory)

	=== How to use ===		=== How to use ===

imported>AlexanderGoesmann at 14:41, 6 January 2006

2006-01-06T14:41:14Z

← Older revision		Revision as of 16:41, 6 January 2006
Line 21:		Line 21:
	=== Requirements ===		=== Requirements ===
	* GlobalConfig.pm (''GENDB/Common'')		* GlobalConfig.pm (''GENDB/Common'')
	* TransTerm.pm (''GENDB/Tools'')		* [[Media:GenDBWiki$$DeveloperDocumentation$$ToolIntegration$TransTerm.pm\|TransTerm].pm] (''GENDB/Tools'')
	* create_generic_tool_TransTerm.pl (''GENDB/exec'')		* [[Media:GenDBWiki$$DeveloperDocumentation$$ToolIntegration$create_generic_tool_TransTerm.pl\|create_generic_tool_TransTerm.pl]] (''GENDB/exec'')

	=== How to use ===		=== How to use ===

imported>AlexanderGoesmann at 14:36, 6 January 2006

2006-01-06T14:36:03Z

← Older revision		Revision as of 16:36, 6 January 2006
Line 10:		Line 10:
	Before you can use ''submit_job.pl'' you have to start a dispatcher (located in GENDB/bin directory).		Before you can use ''submit_job.pl'' you have to start a dispatcher (located in GENDB/bin directory).

	Example: '''/>dispatcher.pl -l ~~/vol~~/tmp/~~transterm~~.log '''		Example: '''/>dispatcher.pl -l /tmp/dispatcher.log '''
	<br>		<br>
	<br>		<br>

imported>DanijelWetter at 12:52, 23 June 2005

2005-06-23T12:52:49Z

← Older revision		Revision as of 14:52, 23 June 2005
Line 10:		Line 10:
	Before you can use ''submit_job.pl'' you have to start a dispatcher (located in GENDB/bin directory).		Before you can use ''submit_job.pl'' you have to start a dispatcher (located in GENDB/bin directory).

	Example: '''>dispatcher.pl -l /vol/tmp/transterm.log '''		Example: '''/>dispatcher.pl -l /vol/tmp/transterm.log '''
	<br>		<br>
	<br>		<br>

imported>DanijelWetter at 12:51, 23 June 2005

2005-06-23T12:51:39Z

← Older revision		Revision as of 14:51, 23 June 2005
Line 25:		Line 25:

	=== How to use ===		=== How to use ===
	Create a generic tool instance of TransTerm. For that task use the script ''create_generic_tool_TransTerm.pl''. ~~You have to determine~~ a GenDB project, ~~further~~ parameters ~~are optional~~ (Default tool name is "TransTerm").		Create a generic tool instance of TransTerm. For that task use the script ''create_generic_tool_TransTerm.pl''. Mandatory parameter is a GenDB project, for optional parameters see usage. (Default tool name is "TransTerm")

	Example: '''>gendb_start -l create_generic_tool_TransTerm.pl -p GenDB_DEMO-2.2'''		Example: '''/>gendb_start create_generic_tool_TransTerm.pl -p GenDB_DEMO-2.2'''

	With ''submit_job.pl'' (located in GENDB/share/exec directory) you can run TransTerm. You have to determine a GenDB project, a contig and tool name. Use the tool name which was set with ''create_generic_tool_TransTerm.pl'' before. Make sure a dispatcher is running!		With ''submit_job.pl'' (located in GENDB/share/exec directory) you can run TransTerm. You have to determine a GenDB project, a contig and tool name. Use the tool name which was set with ''create_generic_tool_TransTerm.pl'' before. Make sure a dispatcher is running!

	Example: '''>gendb_start -l submit_job.pl -p GenDB_DEMO-2.2 -c pSymB -t TransTerm -a'''		Example: '''/>gendb_start submit_job.pl -p GenDB_DEMO-2.2 -c pSymB -t TransTerm -a'''

	=== References ===		=== References ===
	* http://www.tigr.org/software/transterm.html		* http://www.tigr.org/software/transterm.html
	* Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith and Steven L. Salzberg. Prediction of Transcription Terminators in Bacterial Genomes. ''J Mol Biol'' 301, (1), 27-33 (2000)		* Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith and Steven L. Salzberg. Prediction of Transcription Terminators in Bacterial Genomes. ''J Mol Biol'' 301, (1), 27-33 (2000)

imported>DanijelWetter at 12:40, 23 June 2005

2005-06-23T12:40:40Z

← Older revision		Revision as of 14:40, 23 June 2005
Line 27:		Line 27:
	Create a generic tool instance of TransTerm. For that task use the script ''create_generic_tool_TransTerm.pl''. You have to determine a GenDB project, further parameters are optional (Default tool name is "TransTerm").		Create a generic tool instance of TransTerm. For that task use the script ''create_generic_tool_TransTerm.pl''. You have to determine a GenDB project, further parameters are optional (Default tool name is "TransTerm").

	Example: '''>gendb_start -l create_generic_tool_TransTerm.pl -p GenDB_DEMO-2.2 ~~-n TransTerm_99 -g -c 99~~'''		Example: '''>gendb_start -l create_generic_tool_TransTerm.pl -p GenDB_DEMO-2.2'''

	With ''submit_job.pl'' (located in GENDB/share/exec directory) you can run TransTerm. You have to determine a GenDB project, a contig and tool name. Use the tool name which was set with ''create_generic_tool_TransTerm.pl'' before. Make sure a dispatcher is running!		With ''submit_job.pl'' (located in GENDB/share/exec directory) you can run TransTerm. You have to determine a GenDB project, a contig and tool name. Use the tool name which was set with ''create_generic_tool_TransTerm.pl'' before. Make sure a dispatcher is running!

	Example: '''>gendb_start -l submit_job.pl -p GenDB_DEMO-2.2 -c pSymB -t ~~TransTerm_99~~ -a'''		Example: '''>gendb_start -l submit_job.pl -p GenDB_DEMO-2.2 -c pSymB -t TransTerm -a'''

	=== References ===		=== References ===
	* http://www.tigr.org/software/transterm.html		* http://www.tigr.org/software/transterm.html
	* Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith and Steven L. Salzberg. Prediction of Transcription Terminators in Bacterial Genomes. ''J Mol Biol'' 301, (1), 27-33 (2000)		* Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith and Steven L. Salzberg. Prediction of Transcription Terminators in Bacterial Genomes. ''J Mol Biol'' 301, (1), 27-33 (2000)

imported>DanijelWetter at 12:33, 23 June 2005

2005-06-23T12:33:32Z

← Older revision		Revision as of 14:33, 23 June 2005
Line 22:		Line 22:
	* GlobalConfig.pm (''GENDB/Common'')		* GlobalConfig.pm (''GENDB/Common'')
	* TransTerm.pm (''GENDB/Tools'')		* TransTerm.pm (''GENDB/Tools'')
	* create_generic_tool_TransTerm.pl (''GENDB/~~Tools~~'')		* create_generic_tool_TransTerm.pl (''GENDB/exec'')

	=== How to use ===		=== How to use ===

imported>DanijelWetter at 12:32, 23 June 2005

2005-06-23T12:32:42Z

← Older revision		Revision as of 14:32, 23 June 2005
Line 10:		Line 10:
	Before you can use ''submit_job.pl'' you have to start a dispatcher (located in GENDB/bin directory).		Before you can use ''submit_job.pl'' you have to start a dispatcher (located in GENDB/bin directory).

	Example: '''>dispatcher -l /vol/tmp/transterm.log '''		Example: '''>dispatcher.pl -l /vol/tmp/transterm.log '''
	<br>		<br>
	<br>		<br>

imported>DanijelWetter at 12:31, 23 June 2005

2005-06-23T12:31:27Z

← Older revision		Revision as of 14:31, 23 June 2005
Line 10:		Line 10:
	Before you can use ''submit_job.pl'' you have to start a dispatcher (located in GENDB/bin directory).		Before you can use ''submit_job.pl'' you have to start a dispatcher (located in GENDB/bin directory).

	Example: '''>dispatcher -l /vol/tmp/transterm.log '''		Example: '''>dispatcher -l /vol/tmp/transterm.log '''
	<br>		<br>
	<br>		<br>
Line 27:		Line 27:
	Create a generic tool instance of TransTerm. For that task use the script ''create_generic_tool_TransTerm.pl''. You have to determine a GenDB project, further parameters are optional (Default tool name is "TransTerm").		Create a generic tool instance of TransTerm. For that task use the script ''create_generic_tool_TransTerm.pl''. You have to determine a GenDB project, further parameters are optional (Default tool name is "TransTerm").

	Example: '''>gendb_start -l create_generic_tool_TransTerm.pl -p GenDB_DEMO-2.2 -n TransTerm_99 -g -c 99'''		Example: '''>gendb_start -l create_generic_tool_TransTerm.pl -p GenDB_DEMO-2.2 -n TransTerm_99 -g -c 99'''

	With ''submit_job.pl'' (located in GENDB/share/exec directory) you can run TransTerm. You have to determine a GenDB project, a contig and tool name. Use the tool name which was set with ''create_generic_tool_TransTerm.pl'' before. Make sure a dispatcher is running!		With ''submit_job.pl'' (located in GENDB/share/exec directory) you can run TransTerm. You have to determine a GenDB project, a contig and tool name. Use the tool name which was set with ''create_generic_tool_TransTerm.pl'' before. Make sure a dispatcher is running!

	Example: '''>gendb_start -l submit_job.pl -p GenDB_DEMO-2.2 -c pSymB -t TransTerm_99 -a'''		Example: '''>gendb_start -l submit_job.pl -p GenDB_DEMO-2.2 -c pSymB -t TransTerm_99 -a'''

	=== References ===		=== References ===
	* http://www.tigr.org/software/transterm.html		* http://www.tigr.org/software/transterm.html
	* Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith and Steven L. Salzberg. Prediction of Transcription Terminators in Bacterial Genomes. ''J Mol Biol'' 301, (1), 27-33 (2000)		* Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith and Steven L. Salzberg. Prediction of Transcription Terminators in Bacterial Genomes. ''J Mol Biol'' 301, (1), 27-33 (2000)